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Deciphering the in vivo RNA structure code in regulating protein translation in plants (DING_J22DTP2)


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  Dr Y Ding  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Codon optimisation is a common method in synthetic biology to achieve high levels of protein expression. It relies on the creation of so-called “silent” or synonymous mutations within a coding sequence, such that the DNA/RNA sequence is altered but the resulting amino acid sequence remains unchanged. Codon optimisation mainly takes into account codon usage bias (i.e. which of the 61 codons encoding for one of 20 amino acids are preferentially used in a given species), although more sophisticated online tools also use additional parameters such as GC content, mRNA structure, repetitive sequences and inadvertent introduction of regulatory cis-elements.

This project will study the effect of synonymous mutations on in vivo RNA structure and how this can be used to improve codon optimisation to achieve greater control over transgene expression in plants. The project will define the structure of RNA species in vivo and compare this to phenotypic analysis of synonymous mutants in plants. This work will be essential to shed new light on how synonymous mutations influence RNA structure and thus protein function in living cells. The student will receive extensive training in molecular biology, synthetic biology, nucleic acid chemistry and bioinformatics. The successful applicant will enjoy the benefits of working at both the John Innes Centre and the University of East Anglia.

The Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP) is open to UK and international candidates for entry October 2021 and offers postgraduates the opportunity to undertake a 4-year PhD research project whilst enhancing professional development and research skills through a comprehensive training programme. You will join a vibrant community of world-leading researchers. All NRPDTP students undertake a three-month professional internship placement (PIPS) during their study. The placement offers exciting and invaluable work experience designed to enhance professional development. Full support and advice will be provided by our Professional Internship team. Students with, or expecting to attain, at least an upper second class honours degree, or equivalent, are invited to apply.

This project has been shortlisted for funding by the NRPDTP programme. Shortlisted applicants will be interviewed on Tuesday 25th January, Wednesday 26th January and Thursday 27th January 2022.

Visit our website for further information on eligibility and how to apply: https://biodtp.norwichresearchpark.ac.uk/

Our partners value diverse and inclusive work environments that are positive and supportive. Students are selected for admission without regard to gender, marital or civil partnership status, disability, race, nationality, ethnic origin, religion or belief, sexual orientation, age or social background.


Funding Notes

This project is awarded with a 4-year Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP) PhD studentship. The studentship includes payment of tuition fees (directly to the University), a stipend for each year of the studentship (2021/2 stipend rate: £15,609), and a Research Training Support Grant for each year of the studentship of £5,000 p.a.

References

1. Feike, D., Korolev, A. V., Soumpourou, E., Murakami, E., Reid, D., Breakspear, A., Rogers, C., Radutoiu, S., Stougaard, J., Harwood, W. A., Oldroyd, G. E. D. & Miller, J. B. Characterizing standard genetic parts and establishing common principles for engineering legume and cereal roots. Plant Biotechnol J 17, 2234-2245, (2019).
2. Yang, M., Woolfenden, H. C., Zhang, Y., Fang, X., Liu, Q., Vigh, M. L., Cheema, J., Yang, X., Norris, M., Yu, S., Carbonell, A., Brodersen, P., Wang, J. & Ding, Y. Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo. Nucleic Acids Res 48, 8767-8781, (2020).
3. Zhang, H. & Ding, Y. Novel insights into the pervasive role of RNA structure in post-transcriptional regulation of gene expression in plants. Biochem Soc Trans 49, 1829-1839, (2021).
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